Carlson Prunus serotina Unigene v1.0 (Penn State)

Overview
Analysis NameCarlson Prunus serotina Unigene v1.0 (Penn State)
Unigene NameCarlson Prunus serotina Unigene v1
MethodNewbler (v2.5)
Source1.3M 454 FLX reads
Date performed2012-09-30

The Prunus serotina (black cherry) EST data hosted by the Genome Database for Rosaceae (GDR) was compiled and analyzed by John Carlson's lab at Penn State Uniersity.   The goal of this project was to develop genomic resources for black cherry (Prunus serotina Ehrh.), an economically and ecologically valuable hardwood tree native to the eastern United States.  The objectives of the project were to 

  1. Develop a sequence database for expressed genes in black cherry emphasizing response to ozone stress; 
  2. Construct a genetic linkage map for a full-sib population to serve as a reference map for the species, and 
  3. Identify QTL for quantitative variation in sensitivity to ozone in black cherry.

The data set consists of 249,464,869 bases of cDNA sequence from 1,335,589 454 sequence reads obtained by Roche-454 FLX sequencing of two cDNA preparations from leaf tissues of 5 ozone-sensitive black cherry plants and 5 ozone-tolerant plants that had been exposed to 80 ppm ozone under controlled conditions for app. one month.  The ozone-treated seedlings were progeny of an ozone tolerant seed tree (genotype “MO-21”) and an ozone sensitive mother tree (genotype “R-14”) from a first generation black cherry seed orchard in the PA Bureau of Forestry’s Penn Nursery. 

The sequences assembled into 28,461 transcript contigs representing 17,781 unique expressed genes.  BLAST alignment showed that 83% of the black cherry genes had highest level of homology with Prunus persica genes.  App. 12% of the expressed genes were functionally annotated as having a potential role in response to stresses or to biotic and abiotic stimuli. 

We identified over 2,000 high quality microsatellite DNA markers in the black cherry transcript contigs, of which 1374 SSR loci were polymorphic in our mapping populations from the R-14 and MO-21 genotypes.  We also identified 36,151 high-confidence SNPs from the EST dataset.  The SSR and SNP markers are currently being used to produce a reference genetic linkage map with a family of 120 full-sib plants which segregate for ozone sensitivity.   We hope that this data for Prunus serotina will lead to new tools for tree improvement and forest management of black cherry, as well a useful community resource for comparative and functional genomics. This project was supported by a grant from the USDA NIFA Plant Genome Program (#2008-35300-19234).

 

Newbler Processing Summary
Number of reads available 1,335,589
Number of aligned reads 1,149,700 (86.08%)
Number of aligned bases 214,413,175 (85.95%)
Number of contigs 28,461
Total length of contigs 12,617,573 bp
Averge contig size (isotigs/large contigs) 806 / 913 bp
Number of Putative Unigenes 17,781

 

Contact
Contact Details
 Name  John E. Carlson
 Lab  The Schatz Center for Tree Molecular Genetics
 Organization  Penn State University
 Address  323 Forest Resources Building, University Park, PA 16802
 Telephone  814-863-9164
 Fax  814-863-3725
 Email  jec16@psu.edu

 

Publication
Details
Title An EST database for study of ozone stress-response in Prunus serotina
Authors Teodora Orendovici Best, Charles Addo-Quaye, Donghwan Shim, D. Scott DiLoreto, Tyler K. Wagner, and John E. Carlson 
Status In preparation

 

 

Downloads
 Available Files
 454 EST reads   P_serotina-Carlson-GI9L74W01.sff.gz
 P_serotina-Carlson-GI9L74W02.sff.gz
 Newbler All contigs FASTA  P_serotina-Carlson-454AllContigs.fna.gz
 Newbler All contigs QUAL  P_serotina-Carlson-454AllContigs.qual.gz